The evolution of HIV-1 was examined by longitudinal phylogenetic analysis of the V3 region of the HIV env gene in six hemophiliac children and adolescents. The participants were selected based on the trajectory of CD4 T-cell decline during the first two years following study enrollment. Major findings were that individuals with similar clinical courses have distinctively different levels of viral diversity during the latent asymptomatic period through CD4 T-cell decline, suggesting differential immune pressures driving the rate of quasispecies evolution. Two divergent populations of HIV in a single patient, one with macrophage- and the other with T-cell-tropic genotypic features, were observed co-existing over multiple timepoints with different levels of diversity. The T-tropic clades trended towards an increasing accumulation of basic residues and may have a higher affinity for the CXCR4 receptor. We have also confirmed the findings of others that there is a strong trend towards positive selection for change when CD4 T-cell counts were greater than 200.